Disable cPanel's .htaccess abilities

I was attempting to set up Hotlink Protection via cPanel today, however it kept giving me an error because I have custom defined mod_rewrite rules in the .htaccess already. After reading through some forum posts on Google, it seems like people have had cPanel mess with their .htaccess, or there .htaccess messes with some cPanel configurations.

Is their a way, either through WHM or cPanel, to disable it's ability to modify .htacess? Even better would be a way to do this only on specific directories? The best option would be one that shows me exactly what cPanel is about to do in .htaccess, and prompt me whether or not I want to continue. That's probably unlikely, but maybe should be considered for future releases.